Nearly all virulence factors in Bordetella pertussis are activated by a master two-component system, BvgAS, composed of the sensor kinase BvgS and the response regulator BvgA. When BvgS is active, BvgA is phosphorylated, and virulence activated genes are expressed the Bvg(+) mode. When BvgS is inactive and BvgA is not phosphorylated, virulence repressed genes are induced the Bvg(-) mode. The Bvg(i) mode represents an intermediate state, with an intermediate concentration of BvgAP where kinase-on and kinase-off BvgS proteins may co-exist in equilibrium. Virulence genes include those encoding adhesins, such as the fimbrial subunits fim2 and fim3, which are needed to adhere to the ciliated epithelial cells within the upper respiratory tract, and toxins, which cause the major symptoms of whooping cough disease. Several of these BvgA-activated gene products are components of the acellular pertussis vaccine used in the U.S. and Western Europe. The genes for fim2 and fim3 undergo on/off phase variation independently of each other via variation in the length of a C-stretch in their promoters. These fim promoters are also part of the BvgAS virulence regulon and therefore, if in an on configuration, are activated by phosphorylated BvgA under normal growth conditions Bvg(+) mode but not in the Bvg(-) mode. In the B. pertussis Tohama I strain (FIM2+/FIM3-) the fim3 promoter is in the off state. Nevertheless, a high level of fim3 RNA is observed in the Bvg(-) mode. We have determined the explanation for this anomalous behavior by defining a Bvg-repressed promoter (BRP), located 400 bp upstream of the Pfim3 transcriptional start. Although transcription of the fim3 gene in the Bvg(-) results in Fim3 translation as measured by a LacZ translational fusion, no accumulation of Fim3 protein is detectable. We propose that Fim3 protein resulting from translation of message driven by BRP in the Bvg(-) mode is unstable due to the lack of the fimbrial assembly apparatus encoded by the fimBC genes and therefore not expressed in the Bvg(-) mode.